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pmid:39975557
Interactions between NAD+ metabolism and immune cell infiltration in ulcerative colitis: subtype identification and development of novel diagnostic models.
Linglin Tian · Huiyang Gao · Tian Yao · Yuhao Chen · Linna Gao · Jingxiang Han · Lanqi Zhu · He Huang
Frontiers in immunology · 2025 doi:10.3389/fimmu.2025.1479421
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Experiment
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Complete file
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Growing evidence highlights the pivotal role of nicotinamide adenine dinucleotide (NAD+) metabolism in UC pathogenesis, prompting our investigation into the subtype-specific molecular underpinnings and diagnostic potential of NAD+ metabolism-related genes (NMRGs).\nMethods: Transcriptome data from UC patients and healthy controls were downloaded from the GEO database, specifically GSE75214 and GSE87466. We performed unsupervised clustering based on differentially expressed NAD+ metabolism-related genes (DE-NMRGs) to classify UC cases into distinct subtypes. GSEA and GSVA identified potential biological pathways active within these subtypes, while the CIBERSORT algorithm assessed differential immune cell infiltration. Weighted gene co-expression network analysis (WGCNA) combined with differential gene expression analysis was used to pinpoint specific NMRGs in UC. Robust gene features for subtyping and diagnosis were selected using two machine learning algorithms. Nomograms were constructed and their effectiveness was evaluated using receiver operating characteristic (ROC) curves. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) was conducted to verify gene expression in cell lines.\nResults: In our study, UC patients were classified into two subtypes based on DE-NMRGs expression levels, with Cluster A exhibiting enhanced self-repair capabilities during inflammatory responses and Cluster B showing greater inflammation and tissue damage. Through comprehensive bioinformatics analyses, we identified four key biomarkers (AOX1, NAMPT, NNMT, PTGS2) for UC subtyping, and two (NNMT, PARP9) for its diagnosis. These biomarkers are closely linked to various immune cells within the UC microenvironment, particularly NAMPT and PTGS2, which were strongly associated with neutrophil infiltration. Nomograms developed for subtyping and diagnosis demonstrated high predictive accuracy, achieving area under curve (AUC) values up to 0.989 and 0.997 in the training set and up to 0.998 and 0.988 in validation sets. RT-qPCR validation showed a significant upregulation of NNMT and PARP9 in inflamed versus normal colonic epithelia, underscoring their diagnostic relevance.\nConclusion: Our study reveals two NAD+ subtypes in UC, identifying four biomarkers for subtyping and two for diagnosis. These findings could suggest potential therapeutic targets and contribute to advancing personalized treatment strategies for UC, potentially improving patient outcomes.", "claims": [{"id": "claim-method", "statement": "Differential expression analysis between UC and normal samples in the training set was conducted using limma package (39), with significant differential expression defined by |log2 fold change (FC)| > 0.5 and false discovery rate (FDR) < 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39975557", "locator": "sections[5] \"Identification and enrichment analysis of differentially expressed genes between UC and normal\" paragraph 2", "quote": "Differential expression analysis between UC and normal samples in the training set was conducted using limma package (39), with significant differential expression defined by |log2 fold change (FC)| > 0.5 and false discovery rate (FDR) < 0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39975557", "locator": "sections[27] \"Data availability statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified two NAD+ metabolism-related subtypes of ulcerative colitis, four biomarkers for subtyping (AOX1, NAMPT, NNMT, PTGS2), and two diagnostic biomarkers (NNMT, PARP9).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39975557", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "In our study, UC patients were classified into two subtypes based on DE-NMRGs expression levels, with Cluster A exhibiting enhanced self-repair capabilities during inflammatory responses and Cluster B showing greater inflammation and tissue damage."}, {"asset": "source:pmid:39975557", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Through comprehensive bioinformatics analyses, we identified four key biomarkers (AOX1, NAMPT, NNMT, PTGS2) for UC subtyping, and two (NNMT, PARP9) for its diagnosis."}, {"asset": "source:pmid:39975557", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Nomograms developed for subtyping and diagnosis demonstrated high predictive accuracy, achieving area under curve (AUC) values up to 0.989 and 0.997 in the training set and up to 0.998 and 0.988 in validation sets."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified two NAD+ metabolism-related subtypes of ulcerative colitis, four biomarkers for subtyping (AOX1, NAMPT, NNMT, PTGS2), and two diagnostic biomarkers (NNMT, PARP9).", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:39975557"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE206285"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE206285"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39975557", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2025.1479421", "sha256": "sha256:bb725163dd9ca8ddf42f673545ebd64e09cdb93cc825dbe3b0671bb2e26ae3fa", "bytes": 48749, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2025.1479421", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11835821", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE206285", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE206285", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE206285", "version": null, "note": "Publicly available datasets were analyzed in this study. 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